[…] (dimers) and those extracted from higher order complexes (K-mers), from information available in the PDB.We filtered the DIMER70 list in order to reduce the redundancy between monomers to 25%, using PISCES (http://dunbrack.fccc.edu/PISCES.php) [] with the following input parameters: sequence percentage identity <25%, resolution <3Å, R-factor <0.3, sequence length between 40 and 10,000, include no […]

library_books

A novel secondary structure based on fused five membered rings motif

2016

Sci Rep

PMCID: 4980606

PMID: 27511362

DOI: 10.1038/srep31483

[…] A non-redundant dataset of 4114 protein chains present in 3976 PDB (Protein Data Bank), files were selected using PISCES server, such that the resolution ≤2 Å, R-factor is ≤0.2, and the sequence identity between any two protein sequences is ≤25%. The files used are given in. REDUCE was used to fix the hydrogen po […]

call_split

Ab Initio Coordination Chemistry for Nickel Chelation Motifs

[…] uctures were considered and all NMR and theoretical models were excluded. The initial dataset comprised about 928 crystal structures. The dataset was further was culled at 40% sequence identity using PISCES server [] to remove redundant structures due to homodimers and identical entries. Other threshold parameters employed included resolution between 0.0–3.0Å and R value of 0.3. The resulting cull […]

[…] y, because the high similarity data will lead to overestimating the performance of the proposed predictors.In order to exclude highly similar sequences from these datasets, BLASTClust, CD-HIT [], and PISCES [] have been developed and could be freely obtained at the addresses listed in . BLASTClust is a program that can be used to cluster either protein or nucleotide sequences. However, since it re […]

library_books

An Overview of the Prediction of Protein DNA Binding Sites

2015

Int J Mol Sci

PMCID: 4394471

PMID: 25756377

DOI: 10.3390/ijms16035194

[…] subsequences of other proteins in a data set were eliminated. The frequently used clustering program contains blastclust (available from the National Center for Biotechnology Information, NCBI), the PISCES Web server [], and the H-CD-HIT program []. Using the metaDBSite method, the protein–DNA complexes with a resolution better than 3.0 Å were submitted to H-CD-HIT to obtain a nonredundant data s […]